Skip to main content
NCBI home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1983 Apr 11;11(7):2121–2134. doi: 10.1093/nar/11.7.2121

Proton exchange rates in transfer RNA as a function of spermidine and magnesium.

J S Tropp, A G Redfield
PMCID: PMC325866  PMID: 6340067

Abstract

Solvent exchange rates of selected protons were measured by NMR saturation recovery for E. coli tRNAVal, E. colifMet and yeast tRNAPhe, at temperatures from 20 to 40 degrees C, in the presence of 0.12M Na+ and various levels of added spermidine. tRNAVal was also studied with added Mg++. The exchange rates in zero spermidine and Mg++ indicate early melting of the U8 A14 interaction, in accord with thermodynamic melting studies. Exchange rates for secondary protons suggest early melting of the T stem in tRNAfMet and the acceptor stem in tRNAPhe, in contradiction with melting transition assignments from thermodynamic work. Addition of 10 spermidines per tRNA stabilizes the secondary and tertiary interactions more effectively than added Na+, but less so than Mg++. Added spermidine has the curious effect of increasing the exchange rate of the psi 55 N1 proton, while protecting the psi 55 N3 proton from exchange in all three tRNA's. Added Mg++ has the same effect on tRNAVal.

Full text

PDF
2121

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Bolton P. H., Kearns D. R. Effect of cations on tRNA structure. Biochemistry. 1977 Dec 27;16(26):5729–5741. doi: 10.1021/bi00645a013. [DOI] [PubMed] [Google Scholar]
  2. Coutts S. M., Riesner D., Römer R., Rabl C. R., Maass G. Kinetics of conformational changes in tRNA Phe (yeast) as studied by the fluorescence of the Y-base and of formycin substituted for the 3'-terminal adenine. Biophys Chem. 1975 Oct;3(4):275–289. doi: 10.1016/0301-4622(75)80020-2. [DOI] [PubMed] [Google Scholar]
  3. Crothers D. M., Cole P. E., Hilbers C. W., Shulman R. G. The molecular mechanism of thermal unfolding of Escherichia coli formylmethionine transfer RNA. J Mol Biol. 1974 Jul 25;87(1):63–88. doi: 10.1016/0022-2836(74)90560-9. [DOI] [PubMed] [Google Scholar]
  4. Daniel W. E., Jr, Cohn M. Proton nuclear magnetic resonance of spin-labeled Escherichia coli tRNAf1MET. Proc Natl Acad Sci U S A. 1975 Jul;72(7):2582–2586. doi: 10.1073/pnas.72.7.2582. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Hare D. R., Reid B. R. Direct assignment of the dihydrouridine-helix imino proton resonances in transfer ribonucleic acid nuclear magnetic resonance spectra by means of the nuclear Overhauser effect. Biochemistry. 1982 Apr 13;21(8):1835–1842. doi: 10.1021/bi00537a020. [DOI] [PubMed] [Google Scholar]
  6. Hinz H. J., Filimonov V. V., Privalov P. L. Calorimetric studies on melting of tRNA Phe (yeast). Eur J Biochem. 1977 Jan 3;72(1):79–86. doi: 10.1111/j.1432-1033.1977.tb11226.x. [DOI] [PubMed] [Google Scholar]
  7. Hurd R. E., Reid B. R. Helix-coil dynamics in RNA: the amino acid acceptor helix of Escherichia coli phenylalanine transfer RNA. J Mol Biol. 1980 Sep 15;142(2):181–193. doi: 10.1016/0022-2836(80)90044-3. [DOI] [PubMed] [Google Scholar]
  8. Johnston P. D., Redfield A. G. An NMR study of the exchange rates for protons involved in the secondary and tertiary structure of yeast tRNA Phe. Nucleic Acids Res. 1977 Oct;4(10):3599–3615. doi: 10.1093/nar/4.10.3599. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Johnston P. D., Redfield A. G. Pulsed FT-NMR double resonance studies of yeast tRNAPhe: specific nuclear Overhauser effects and reinterpretation of low temperature relaxation data. Nucleic Acids Res. 1978 Oct;5(10):3913–3927. doi: 10.1093/nar/5.10.3913. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Johnston P. D., Redfield A. G. Study of transfer ribonucleic acid unfolding by dynamic nuclear magnetic resonance. Biochemistry. 1981 Jul 7;20(14):3996–4006. doi: 10.1021/bi00517a008. [DOI] [PubMed] [Google Scholar]
  11. Kastrup R. V., Schmidt P. G. 1H nuclear magnetic resonance of modified bases of valine transfer ribonucleic acid (Escherichia coli). A direct monitor of sequential thermal unfolding. Biochemistry. 1975 Aug 12;14(16):3612–3618. doi: 10.1021/bi00687a015. [DOI] [PubMed] [Google Scholar]
  12. Privalov P. L., Filimonov V. V. Thermodynamic analysis of transfer RNA unfolding. J Mol Biol. 1978 Jul 15;122(4):447–464. doi: 10.1016/0022-2836(78)90421-7. [DOI] [PubMed] [Google Scholar]
  13. Reid B. R., McCollum L., Ribeiro N. S., Abbate J., Hurd R. E. Identification of tertiary base pair resonances in the nuclear magnetic resonance spectra of transfer ribonucleic acid. Biochemistry. 1979 Sep 4;18(18):3996–4005. doi: 10.1021/bi00585a024. [DOI] [PubMed] [Google Scholar]
  14. Sakai T. T., Cohen S. S. Effects of polyamines on the structure and reactivity of tRNA. Prog Nucleic Acid Res Mol Biol. 1976;17:15–42. doi: 10.1016/s0079-6603(08)60064-1. [DOI] [PubMed] [Google Scholar]
  15. Sakai T. T., Torget R., I J., Freda C. E., Cohen S. S. The binding of polyamines and of ethidium bromide to tRNA. Nucleic Acids Res. 1975 Jul;2(7):1005–1022. doi: 10.1093/nar/2.7.1005. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Stein A., Crothers D. M. Conformational changes of transfer RNA. The role of magnesium(II). Biochemistry. 1976 Jan 13;15(1):160–168. doi: 10.1021/bi00646a025. [DOI] [PubMed] [Google Scholar]
  17. Teitelbaum H., Englander S. W. Open states in native polynucleotides. I. Hydrogen-exchange study of adenine-containing double helices. J Mol Biol. 1975 Feb 15;92(1):55–78. doi: 10.1016/0022-2836(75)90091-1. [DOI] [PubMed] [Google Scholar]
  18. Tropp J., Redfield A. G. Environment of ribothymidine in transfer ribonucleic acid studied by means of nuclear Overhauser effect. Biochemistry. 1981 Apr 14;20(8):2133–2140. doi: 10.1021/bi00511a010. [DOI] [PubMed] [Google Scholar]
  19. Urbanke C., Römer R., Maass G. Tertiary structure of tRNAPhe (yeast): kinetics and electrostatic repulsion. Eur J Biochem. 1975 Jul 1;55(2):439–444. doi: 10.1111/j.1432-1033.1975.tb02180.x. [DOI] [PubMed] [Google Scholar]
  20. Urbanke C., Römer R., Maass G. The binding of ethidium bromide to different conformations of tRNA. Unfolding of tertiary structure. Eur J Biochem. 1973 Mar 15;33(3):511–516. doi: 10.1111/j.1432-1033.1973.tb02710.x. [DOI] [PubMed] [Google Scholar]

Articles from Nucleic Acids Research are provided here courtesy of Oxford University Press

RESOURCES